chimpanzee gut metagenome
Fecal samples (solid phase) were re-suspended and diluted (50%) in phosphate buffered saline (PBS) and then centrifuged at 2500 g for 20 minutes. The supernatant was then filtered using an 0.45M filter. To enrich for viral particles by reduction of host background, stool supernatant was filtered through a 0.45-m filter (Corning Costar Spin-X centrifuge tube filters), and an aliquot of 315 l of filtrate was pretreated before extraction by incubation with different nucleases: TURBO DNase (Invitrogen, Carlsbad, CA); Baseline-ZERO DNase (Ambion, Foster City, CA); Benzonase (NEB); RNAse A (Promega) for 30 min, at 37 C. Total nucleic acids were extracted using Nuclisens EAsymag (Biomerieux) according manufacturers protocol.  For DNA libraries preparation, 25L of extract was used. Depletion of methylated host DNA was performed using NEBNext Microbiome DNA Enrichment Kit (NEB) according to the manufacturer instructions. DNA was then purified using zymo DNA Clean (Zymo) and eluted in 7.5L of sterile water. DNA libraries were prepared using Nextera XT library preparation kit (Illumina).